Atlas3D is a multiplatform visualization tool which allows import, linear transformation, cutting and export of various data formats in 3D atlas space.
There are two atlases (atlas spaces) included in the tool:
1) 32 mouse brain structures 3-D reconstructed as VRML files from “The Mouse Brain in Stereotaxic Coordinates” by Paxinos & Franklin (2001).
2) 62 rat brain structures 3-D reconstructed as VRML files from “The Rat Brain in Stereotaxic Coordinates” by Paxinos & Watson (2005).
The tool is able to build an atlas slice at any arbitrary angle.
Experimental data can be imported in Atlas3D and warped to atlas space, using manual linear registration, with the possibility to scale, rotate, and position the imported data. This facilitates assignment of location and comparative analysis of signal location in tomographic images.
Supported import formats: NIfTI, VRML, PNG, XYZ point-lists, PA, Atlas Package files.
Supported export formats: VRML
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PrerequirementsAny java3d 1.5.1+ enabled platform. NIfTI import requires a videocard with non power of 2 textures support.
Ease of UseIntermediate
Ratings & Reviews
KeywordsVisualization, Java3D, Java, Linear, Brain Atlas, Application, Volume Rendering, Atlas Application, NIfTI-1, VRML, 3D,
External web sitehttp://www.nesys.uio.no/Atlas3D/
PublicationsHjornevik T, Leergaard TB, Darine D, Moldestad O, Dale AM, Willoch F, Bjaalie JG Three-dimensional atlas system for mouse and rat brain imaging data. Frontiers in Neuroinformatics, 2007; 1:4 doi: 10.3389/neuro.11/004.2007
- Jul 07, 2008
- Last Modified:
- Jun 20, 2012